Evaluation of Published Rational siRNA Design Algorithms Using Firefly luciferase Gene as a Reporter

In mammalian RNA interference (RNAi), a limited fraction of the short interfering RNA (siRNA) is capable of successful interference, since the efficiency of RNAi depends highly on the siRNA sequence used. Several different algorithms for selecting functional siRNA sequences have been published. To find a robust siRNA selection procedure by integrating these algorithms, we performed validation studies on some published rational siRNA design algorithms. In this study, we used a single reporter assay with the firefly luciferase gene, since it is likely that the efficiencies of siRNA sequences vary between target genes, partially depending on the detection sensitivity of the expression of each gene. The results suggest that it is best to select siRNAs that generally satisfy a combination of some reliable integrated algorithms. Our results should be considered when conducting RNAi experiments.